Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi

Fungal species belonging to the genus Melampsora (Basidiomycota, Pucciniales) comprise rust pathogens that alternate between Salicaceae and other plant hosts. Species delineation and identification are difficult within this group due to the paucity of observable morphological features. Several Melampsora rusts are highly host-specific and this feature has been used for identification at the species level. However, this criterion is not always reliable since different Melampsora rust species can overlap on one host but specialize on a different one. To date, two different species recognition methods are used to recognize and define species within the Melampsora genus: (i) morphological species recognition, which is based solely on morphological criteria; and (ii) ecological species recognition, which combines morphological criteria with host range to recognize and define species. In order to clarify species recognition within the Melampsora genus, we applied phylogenetic species recognition to Melampsora poplar rusts by conducting molecular phylogenetic analyses on 15 Melampsora taxa using six nuclear and mitochondrial loci. By assessing the genealogical concordance between phylogenies, we identified 12 lineages that evolved independently, corresponding to distinct phylogenetic species. All 12 lineages were concordant with host specialization, but only three belonged to strictly defined morphological species. The estimation of the species tree obtained with Bayesian concordance analysis highlighted a potential co-evolutionary history between Melampsora species and their reciprocal aecial host plants. Within the Melampsora speciation process, aecial host may have had a strong effect on ancestral evolution, whereas telial host specificity seems to have evolved more recently. The morphological characters initially used to define species boundaries in the Melampsora genus are not reflective of the evolutionary and genetic relationships among poplar rusts. In order to construct a more meaningful taxonomy, host specificity must be considered an important criterion for delineating and describing species within the genus Melampsora as previously suggested by ecological species recognition.     

Toward resolving family-level relationships in rust fungi (Uredinales)

Rust fungi (Basidiomycota, Uredinales) consist of more than 7000 species of obligate plant pathogens that possess some of the most complex life cycles in the Eumycota. Traditionally, a limited number of synapomorphic characters and incomplete life-cycle and host-specificity data have hampered phylogenetic inference within the Uredinales. The application of modern molecular characters to rust systematics has been limited, and current contradictions, especially in the deeper nodes, have not yet been resolved. In this study, two nuclear rDNA genes (18S and 28S) were examined across the breadth of the Uredinales to resolve some systematic conflicts and provide a framework for further studies of the group. Three suborders of rusts are recovered. Of the 13 rust families most widely accepted, 8 are supported in full or in part (Coleosporiaceae, Melampsoraceae, Mikronegeriaceae, Phakopsoraceae p.p., Phragmidiaceae, Pileolariaceae, Pucciniaceae, Raveneliaceae), 3 are redundant (Cronartiaceae, Pucciniastraceae, Pucciniosiraceae), and the status of 2 (Chaconiaceae, Uropyxidaceae) could not be resolved. The Mikronegeriaceae and Caeoma torreyae are the most basal rusts sampled. It is concluded that morphology alone is a poor predictor of rust relationships at most levels. Host selection, on the other hand, has played a significant role in rust evolution. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.     

Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi

To determine the phylogenetic placement of the major groups of higher fungi, we sequenced the DNA sequences from the small-subunit ribosomal RNA (18S rRNA) coding regions from Taphrina wiesneri (synonym: T. cerasi) and Saitoella complicata and compared them to 18S rRNA sequences from the oomycetes, chytridiomycetes, zygomycetes, ascomycetes, and basidiomycetes. Here we demonstrate that the ascomycetes have at least two major evolutionary lineages. Taphrina wiesneri and Saitoella complicata form a monophyletic branch that diverged prior to the separation of other ascomycetes. The same treatment could be accorded to Schizosaccharomyces pombe.      

Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences

Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.     

Phylogenetic positions of rust fungi parasitic on ferns: Evidence from 18S rDNA sequence analysis

Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We sequenced the 18S rDNAs of fern rusts (Hyalopsora polypodii andUredinopsis intermedia) and non-fern rusts (Aecidium epimedii, Coleosporium asterum, Ochropsora kraunhiae, Puccinia suzutake andPhysopella ampelopsidis) and analyzed their phylogenetic relationships with other members of the Urediniomycetes. Our bootstrapped neighbor-joining tree obtained from these analyses showed that rust fungi were apparently monophyletic at high confidence level (100% bootstrap confidence). In this molecular phylogenetic tree, the two fern rusts did not occupy the basal position within the rust fungal lineage and did not form a monophyletic lineage. Two species of the Cronartiaceae (Peridermium harknessii, Cronartium ribicola) and one species of the Coleosporiaceae (Coleosporium asterum) grouped with the fern rusts. Therefore, our results suggested that the two fern rusts were not primitive. On the other hand,Mixia osmundae, which is parasitic on the primitive fernOsmunda, was phylogenetically far from the fern rusts.     

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.     

Phylogenetic study of indigenous grapevine leaf rust fungi in North America and biological identity of an invasive grapevine leaf rust fungus in Brazil

Two American grapevine leaf rust (GLR) fungi, Phakopsora muscadiniae and P. uva, were found to be phylogenetically different from Asian-Australasian GLR fungi. In the phylogram based on rDNA region sequences, a clade of the American fungi was sister to an inclusive clade of three autoecious species on Meliosma and a heteroecious species host-alternating between Meliosma and Parthenocissus. An invasive Brazilian GLR fungus (as P. meliosmae-myrianthae) was included in the Asian-Australasian GLR fungi clade, or the clade of the Thai population of Phakopsora sp. It could be assumed that the Brazilian GLR fungus originated from an inadvertently introduced Thai population.     

Phylogenetic relationships in the gymnopoid and marasmioid fungi (Basidiomycetes, euagarics clade)

Three distinct lineages of gymnopoid and marasmioid fungi are recognized in parsimony and Bayesian analyses of nLSU rDNA sequences. One lineage contains the genera Lentinula, Rhodocollybia, Tetrapyrgos, a resurrected and redefined Mycetinis, and two unresolved clades designated /marasmiellus and /gymnopus. /marasmiellus includes the type species of Marasmiellus and is dominated by members of Gymnopus sect. Vestipedes. /gymnopus includes the type species of Gymnopus, Micromphale and Setulipes, and members of Gymnopus sect. Levipedes. A second lineage includes the genera Marasmius s.s. and Crinipellis and represents a redefined /marasmiaceae. A third lineage includes the genera Cylindrobasidium, Flammulina, Gloiocephala, Physalacria, Strobilurus, Xerula and Marasmius sect. Epiphylli and represents /physalacriaceae. One new combination in Rhodocollybia and four new combinations in Mycetinis are proposed. A discussion of the taxonomic implications resulting from the phylogenetic reconstruction is presented.     

Phylogenetic relationships of theJuglandaceae

A cladistic analysis of molecular data from the chloroplast generbcL was used to examine the taxonomic relationships of the walnut family (Juglandaceae). In addition, chemical and morphological data from a previous study byHufford (1992) were incorporated, expanded, and analyzed independently and in combination with the molecular data. The results of these analyses suggest that theJuglandaceae are more closely related to theFagaceae, Betulaceae, Casuarinaceae, andUrticaceae and their relatives (sensuCronquist 1981) than they are to theAnacardiaceae (sensuThorne 1983). However, sequence data fromrbcL also suggest a relationship between the higherHamamelidae and certain families in theRosidae sensuCronquist 1981 (such asRosaceae andRhamnaceae), an outcome which would add credence to the widely accepted view of the polyphyletic nature of theHamamelidae.     

Taxonomy ofPuccinia species causing rust diseases on sugarcane

A taxonomic revision ofPuccinia species causing rust diseases on sugarcane was conducted to clarify their morphological characteristics. Specimens including previously reported species,Puccinia melanocephala, P. kuehnii andPuccinia sp.sensu Muta, 1987, were collected in Japan and the Philippines and borrowed from various herbaria worldwide. Morphological characteristics of these specimens were examined under light and scanning electron microscopes. Comparative morphological studies of the specimens showed that rust fungi infecting sugarcane could be classified into two species,Puccinia melanocephala andP. kuehnii. Puccinia sp.sensu Muta was morphologically identical withP. kuehnii. Results of this study corroborate previous phylogenetic analysis results of D1/D2 regions of LSU rDNA gene. Contribution No. 157, Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba     

New species of rust fungi from Brazil

New species of rust fungi (Basidiomycota, Uredinales) are described from Brazil: Maravalia allophyli on Allophylus sp., the first Maravalia species on Sapindaceae, Puccinia tianguensis on Hyptis sp. (Lamiaceae), Uredo calatheae on Calathea neoviedii (Marantaceae), and Uredo schizolobii on Schizolobium amazonicum (Caesalpiniaceae). Puccinia fuireniphila is proposed as a new name for Puccinia fuirenicola.     

Phylogenetic analysis of rust fungi (Uredinales) from the Colombian Andean region using 28S ribosomal DNA sequences

Rust fungi (Uredinales, Basidiomycetes) are one of the most diverse and economically important plant-obligated parasites. Taxonomy of this group has been under revision during the last years using molecular techniques to define phylogenetic relationships. In this study we evaluated the phylogenetic affinities of a group of 40 rust fungi obtained from different plants in the Colombian Andean region using sequence analysis of the 28S ribosomal DNA, specifically D1/D2 domains. Comparisons were undertaken with sequences of rust fungi from around the world deposited in the GenBank database. An alignment of sequences was used to build a phylogenetic tree through Maximum parsimony analysis. Our results support the taxonomical validity of families Pucciniaceae, Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Mikronegeriaceae, Coleosporiaceae and Cronartiaceae, while Pucciniosiraceae represents redundant taxa with Pucciniaceae. The analyses indicated that Uropyxidaceae, Raveneliaceae, Chaconiaceae and Pucciniastraceae correspond to polyphyletic families. Melampsoraceae appear to be a basal taxon to the Uredinales. Information obtained in this study will be useful to incorporate a higher number of sequences from tropical rust fungi within global efforts to redefine the taxonomy of order Uredinales. Additionally, we propose to give priority to future phylogenetic studies of taxa: Gerwasia, Hemileia, Phragmidium, Prospodium, Puccinia and Uromyces, genera that include a high number of rust fungi from the tropics.     

Phylogenetic relationships within Colchicaceae

Three plastid regions-the rps16 intron, the atpB-rbcL intergenic spacer, and the trnL-F region-in 73 taxa representing all the genera of Colchicaceae except Kuntheria were sequenced to investigate the intrafamilial relationships of the family. In total, the three gene regions, comprising 3830 characters, were analyzed both separately and in a combined matrix. The results did not support the division of the family into two subfamilies, but they did support a core clade of mainly African genera and a grade of Australian, North American, and Asian taxa. One of the four tribes, Iphigenieae, was grossly paraphyletic, and, unexpectedly, Colchicum was nested within Androcymbium. Further, taxa of Gloriosa and Littonia were intermixed.     

Additions to the rust fungi of Argentina

A contribution is made to the rust fungus flora of Argentina: Puccinia baccharidis-boliviensis, P. cordyceps, P. pucarae, and Aecidium hypseocharidicola are described as new species. Cionothrix praelonga, Fromme?lla mexicana var. mexicana, Phakopsora compressa, Prospodium peruvianum, Puccinia amphiospora, P. chaetochloae, P. liabi, P. pappophori, P. sanguinolenta, P. subaquila, Ravenelia havanensis, Uredo leonuri, Uromyces orbicularis, and U. cnidoscoli are new reports for Argentina. New observations on already known species were made: the aecia of Puccinia subaquila and aecia and uredinia of Uromyces cnidoscoli are described for the first time. Senecio hieronymi is a new host for Puccinia lagenophorae. Uredo leonuri belongs to the genus Coleosporium. Melilotus albus is a new host of Uromyces anthyllidis in Argentina.     

Phylogenetic relationships of cyphelloid homobasidiomycetes

The homobasidiomycetes includes the mushroom-forming fungi. Members of the homobasidiomycetes produce the largest, most complex fruiting bodies in the fungi, such as gilled mushrooms ("agarics"), boletes, polypores, and puffballs. The homobasidiomycetes also includes species that produce minute, cup- or tube-shaped "cyphelloid" fruiting bodies, that rarely exceed 1-2 mm diameter. The goal of this study was to estimate the phylogenetic placements of cyphelloid fungi within the homobasidiomycetes. Sequences from the nuclear large subunit (nuc-lsu) ribosomal DNA (rDNA), 5.8S rDNA, and internal transcribed spacers (ITS) 1 and 2 were obtained for 31 samples of cyphelloid fungi and 16 samples of other homobasidiomycetes, and combined with published sequences. In total, 71 sequences of cyphelloid fungi were included, representing 16 genera. Preliminary phylogenetic analyses of a 1477-sequence data set and BLAST searches using sequences of cyphelloid forms as queries were used to identify taxa that could be close relatives of cyphelloid forms. Subsequent phylogenetic analyses of one data set with 209 samples represented by nuc-lsu rDNA sequences (analyzed with parsimony) and another with 38 samples represented by nuc-lsu and 5.8S rDNA sequences (analyzed with parsimony and maximum likelihood) indicated that cyphelloid forms represent a polyphyletic assemblage of reduced agarics (euagarics clade, Agaricales). Unconstrained tree topologies suggest that there have been about 10-12 origins of cyphelloid forms, but evaluation of constrained topologies with the Shimodaira-Hasegawa test suggests that somewhat more parsimonious scenarios cannot be rejected. Whatever their number, the multiple independent origins of cyphelloid forms represent striking cases of parallel evolutionary reduction of complex fungal morphology.     

Notes on some rust fungi in Vietnam

Sixteen rust species and two unconnected Peridermium collected in Vietnam are enumerated. For all the rust species except Hemileia vastarix, Olivea tectonae, and Puccinia thwaitesii, these are the first records of their occurrence in Vietnam. Some taxonomic and pathological considerations are noted for two economically important pine stem rusts.     

中国西北地区锈菌补记

报道了柄锈菌科4个中国新记录,它们是:大西洋胶锈菌Gymnosporangium atlanticum、多被银莲花柄锈菌Puccinia anemones-raddeanae、隐秘柄锈菌Puccinia aphanicondra和旱金莲单胞锈菌Uromyces tropaeoli。每个种的形态特征描述和线条图是基于本国标本。附有简要讨论。